|
| Status |
Public on Apr 20, 2021 |
| Title |
E11_FJW180312003_CE02 |
| Sample type |
SRA |
| |
|
| Source name |
E11.5_whisker follicles cells
|
| Organism |
Mus musculus |
| Characteristics |
Stage: E11.5
cell type: whisker follicles cells
data quality: ok
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single cells were directly sorted into the cell lysis buffer containing RNasein plus (Promega), Cell Lysis Buffer (Roche), NP40 (Thermo), and RNase free water (TaKaRa).
RamDA-seq sequencing libraries were prepared by using the advanced method of RamDA-seq (refer to the Methods section in "Single-cell full-length total RNA sequencing uncovers dynamics of non-polyadenylated RNAs, recursive splicing and enhancer RNAs" DOI: https://doi.org/10.1038/s41467-018-02866-0).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
mEWF-E11_FJW180312003_CE02_S146
|
| Data processing |
FASTQ files were generated using bcl2fastq (v1.0) for NextSeq.
fastq-mcf (version 1.04.807) was used for adapter trimming with the parameters '-L 42 -l 36 -k 4.0 -q 30' for HiSeq 1500, '-L 50 -l 36 -k 4.0 -q 30' for HiSeq 2500 and '-L 75 -l 36 -k 4.0 -q 30' for NextSeq. The reads were mapped to the mouse genome (mm10) using HISAT2 (version 2.0.4) with the parameters '-p 4 --end-to-end'. Transcript levels were quantified as Transcripts Per Kilobase Million (TPM) with Sailfish (version 0.10.0) using GENCODE vM14 annotation file.
outside of the mean minus three standard deviations of the number of mapped reads to a sailfish index (Sailfish) or the number of assigned reads to gene regions (featureCounts, function of Subread version 1.5.0); over 10% reads assigning to mitochondrial RNA (featureCounts); abnormal gene body coverage of sequencing reads by human curation (RseQC, version 2.6.4).
for count table, after convert Ensemble transcript_id to Gene_id, each isoform expression were summarized on gene level.
Genome_build: mm10
Supplementary_files_format_and_content: txt
|
| |
|
| Submission date |
Mar 23, 2020 |
| Last update date |
Apr 20, 2021 |
| Contact name |
Hironobu Fujiwara |
| E-mail(s) |
hironobu.fujiwara@riken.jp
|
| Organization name |
RIKEN
|
| Department |
Center for Biosystems Dynamics Research
|
| Lab |
Laboratory for Tissue Microenvironment
|
| Street address |
2-2-3 Minatojima-minamimachi
|
| City |
Chuo-ku, Kobe |
| ZIP/Postal code |
6500047 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE147372 |
Tracing the origin of hair follicle stem cells |
|
| Relations |
| BioSample |
SAMN14424505 |
| SRA |
SRX7969295 |
